// Copyright 2023 Jimmy Eng
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.


#ifndef _COMETWRITEPERCOLATOR_
#define _COMETWRITEPERCOLATOR_


class CometWritePercolator
{
public:
   CometWritePercolator();
   ~CometWritePercolator();
   static void WritePercolatorHeader(FILE *fpout);
   static bool WritePercolator(FILE *fpout,
                               FILE *fpdb);


private:
   static bool PrintResults(int iWhichQuery,
                            FILE *fpOut,
                            FILE *fpdb,
                            int iPrintTargetDecoy,
                            int iLenDecoyPrefix);
   static void PrintPercolatorSearchHit(int iWhichQuery,
                                    int iWhichResult,
                                    int iPrintTargetDecoy,
                                    Results *pOutput,
                                    FILE *fpOut,
                                    vector<string> vProteinTargets,
                                    vector<string> vProteinDecoys);
   static void CalcNTTNMC(Results *pOutput,
                          int iWhichQuery,
                          int *iNterm,
                          int *iCterm,
                          int *iNMC);
};

#endif
